X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 6.5
Temperature 277.0
Details MPD, pH 6.5, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 400.51 α = 90
b = 400.51 β = 90
c = 175.41 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2011-06-28
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3.45 50 99.4 0.123 -- -- -- 184810 184810 -3.0 -3.0 92.556
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.45 3.54 100.0 0.011 -- 2.3 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
FOURIER SYNTHESIS 3.45 19.902 -- 1.99 184776 184776 9323 99.97 -- 0.154 0.152 0.1918 FROM PDB ENTRY 2VQE
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.45 3.489 -- 348 5734 0.2511 0.3029 -- 100.0
X Ray Diffraction 3.489 3.5298 -- 284 5820 0.2409 0.2802 -- 100.0
X Ray Diffraction 3.5298 3.5727 -- 331 5763 0.2216 0.2742 -- 100.0
X Ray Diffraction 3.5727 3.6176 -- 332 5776 0.2086 0.2579 -- 100.0
X Ray Diffraction 3.6176 3.6649 -- 307 5785 0.2001 0.2529 -- 100.0
X Ray Diffraction 3.6649 3.7148 -- 292 5795 0.1913 0.2427 -- 100.0
X Ray Diffraction 3.7148 3.7675 -- 309 5804 0.1817 0.2286 -- 100.0
X Ray Diffraction 3.7675 3.8234 -- 327 5791 0.1785 0.2483 -- 100.0
X Ray Diffraction 3.8234 3.8827 -- 337 5777 0.1661 0.194 -- 100.0
X Ray Diffraction 3.8827 3.9459 -- 271 5826 0.1604 0.2041 -- 100.0
X Ray Diffraction 3.9459 4.0134 -- 301 5827 0.1543 0.1786 -- 100.0
X Ray Diffraction 4.0134 4.0857 -- 301 5837 0.1445 0.1825 -- 100.0
X Ray Diffraction 4.0857 4.1636 -- 296 5829 0.1481 0.2141 -- 100.0
X Ray Diffraction 4.1636 4.2478 -- 326 5770 0.1477 0.1696 -- 100.0
X Ray Diffraction 4.2478 4.3392 -- 292 5821 0.1439 0.2074 -- 100.0
X Ray Diffraction 4.3392 4.4391 -- 319 5841 0.1471 0.1935 -- 100.0
X Ray Diffraction 4.4391 4.5488 -- 270 5860 0.1416 0.1879 -- 100.0
X Ray Diffraction 4.5488 4.6703 -- 306 5837 0.1342 0.1898 -- 100.0
X Ray Diffraction 4.6703 4.8058 -- 301 5851 0.1307 0.1802 -- 100.0
X Ray Diffraction 4.8058 4.9586 -- 282 5866 0.126 0.158 -- 100.0
X Ray Diffraction 4.9586 5.1329 -- 309 5845 0.1257 0.1698 -- 100.0
X Ray Diffraction 5.1329 5.3347 -- 323 5875 0.1276 0.1578 -- 100.0
X Ray Diffraction 5.3347 5.5724 -- 297 5863 0.1238 0.1709 -- 100.0
X Ray Diffraction 5.5724 5.859 -- 311 5888 0.1199 0.1534 -- 100.0
X Ray Diffraction 5.859 6.2156 -- 338 5851 0.1252 0.156 -- 100.0
X Ray Diffraction 6.2156 6.6786 -- 295 5925 0.1366 0.186 -- 100.0
X Ray Diffraction 6.6786 7.3202 -- 304 5948 0.1325 0.1843 -- 100.0
X Ray Diffraction 7.3202 8.3112 -- 320 5952 0.1409 0.1783 -- 100.0
X Ray Diffraction 8.3112 10.2289 -- 346 5985 0.1583 0.1861 -- 100.0
X Ray Diffraction 10.2289 19.9018 -- 348 6111 0.1863 0.202 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 117.537
Anisotropic B[1][1] -6.3424
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.3424
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.715
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.8
f_plane_restr 0.005
f_chiral_restr 0.061
f_angle_d 0.869
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19152
Nucleic Acid Atoms 32880
Heterogen Atoms 314
Solvent Atoms 582

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
xds Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (phenix.refine: dev_978) Structure Solution
PHENIX (phenix.refine: dev_978) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Xscale data reduction